I bet someone can answer this better, but here's what everyone has said everywhere:
VR6 can get more power, but is more expensive to mod
1.8t gets lots of power off of little money in mods, but can't get the power that say a turboed VR can
As far as the fastest Golf, do you mean stock or modded? Stock, I bet the R32(soon) or GTI VR6 at the moment. Modded, probably those dual engine ones. Disregarding the 20-yr age difference, I bet the fastest Golf ever would be those 9-10-second Rabbits
if you can afford it, i would go with the vr6. i orginaly wanted to get a vr but changed my mind and got a 1.8t, i love it but i bet that pure power is alot better then turbo spool and turbo lag also with a turbo there are just more things to go wrong, in the long run that is
Ahhh yes the never ending question. First try using the search tool above this topic has been cover every which way from Sunday. But I will give my too bits on this as well.
First let's start with a few background questions.
1) Is this your first dub? If so then you don't have much to compare it too. Prior to owning my VR6 I've had a 1.8 8v & a 1.8T. So I knew I wanted the VR6 next.
What sold be was first I was getting a GLX fully loaded. The pure Torque and rumbling sound of the VR6 gave me wood. My 1.8T is quick but I just like a mean sounding dub.
2) Do you plan to do a lot or any mods to the engine? Besides the engine everything else is pretty much the same. Like dirtjumpwill said the 1.8T is easy and has more hop ups available.
3) The VR6 is a stronger engine hence it's a 2.8L and has 6 cylinders. You can slap a supercharger on it (for a nice penny or two) and you have a serious machine.
If you don't plan to do any mods and are just looking for the faster car off the lot it will be the VR6 by a nose. The 1.8T is lighter and has nice top end speed. The VR6 will kill off the start.
Either one you will enjoy them both. My best suggestion is test drive them both. But my gut is you will go with the VR6. If you want to listen to the car & see my VR6 in action I have movies up here http://www.dailyvw.com
Interesting question because I just drove the 2003 1.8T and the (6-speed) 2003 VR6.
The VR6 is pricier but I think a much more satisfying car to drive. The 1.8T feels like an econo car with a fairly nice turbo slapped onto it. Doesn't have the smoothness and low-end torque power of the VR6. Interesting thing about the 6-speed: if you want the same kind of strong pull that you get with the previous year's 5-speed you have to shift more often.
If you buy a used VW- one strong word of advice- buy an extended warranty. These are great cars but realiability isn't their strong suite. I have a 2000 GTI VR6 and laid out $1500 in repairs before deciding to get my 100k extended warranty.